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Datasets list Below is the list of all publications whose data compose our gene expression compendium. For each publication, we also list the number of arrays it had and the abbreviation we gave it, where the abbreviation are used to name the expression clusters from each publication that we used as part of our collection of gene sets. # Publication Abbreviation Arrays Platform Category Samples Interpretation 1 Alizadeh et al. Alizadeh00 134 cDNA (Stanford) B lymphoma B cell lymphomas Differences between various types of B cell lymphomas 2 Armstrong et al. Armstrong01 72 Hu95 (Affymetrix) Leukemia Acute Lymphocytic Leukemia (ALL) Differences between ALL sub-types 3 Bhattacharjee et al. Bhattacharjee01 203 Hu95 (Affymetrix) Lung cancer Normal lung and lung cancer: adenocarcinoma, squamous cell carcinoma and carcinooid Differences between various types of lung cancer and normal lung 4 Blader et al. Blader01 18 cDNA (Stanford) Fibroblast infection Toxoplasma infected human foreskin fibrobalsts Response of fibroblasts to infection 5 Boldrick et al. Boldrick02 183 cDNA (Stanford) Stimulated PBMC Human peripheral blood mononuclear cells responding to bacteria and bacterial products Differences between stimulated and non-stimulated PBMCs and between various types of stimuli 6 Chen et al. Chen02 207 cDNA (Stanford) Liver cancer Hepatitis infected liver and hepatocellular carcinoma Differences between non-tumor (mostly hepaitis) liver and HCC 7 Cuadras et al. Cuadras02 16 cDNA (Stanford) Viral infection Rotavirus infected cells Response of cells to viral infection 8 Detweiler et al. Detweiler01 53 cDNA (Stanford) Stimulated immune Human macrophage cell line (U937) response to Salmonella Differences between mock and bacterial infected cells, both PBMCs and monocytes 9 Garber et al. Garber01 73 cDNA (Stanford) Lung cancer Normal lung and lung cancer: adenocarcinoma, squamous cell carcinoma and carcinooid Differences between various types of lung cancer and normal lung 10 Golub et al. Golub99 70 HuGeneFL (Affymetrix) Leukemia Acute Lymphocytic Leukemia (ALL) and Acute Myelocytic Leukemia (AML) Differences between ALL and AML 11 Iyer et al. Iyer99 18 cDNA (Stanford) Fibroblast serum Serum response in primary human fibroblasts Temporal response of human fibroblasts to serum 12 Lessnick et al. Lessnick02 10 Hu95 (Affymetrix) Fibroblast EWS-FLI Extended lifespan human fibroblasts expressing the EWS/FLI oncogen Temporal response to EWS/FLI induction in fibroblasts 13 Nutt et al. Nutt03 47 Hu95 (Affymetrix) Gliomas Malignant gliomas Differences between various gliomas 14 Perou et al. Perou00 84 cDNA (Stanford) Breast cancer Normal breast, breast cancer, human mammary epithelial cells and breast cancer cell lines Differences between breast tissue, cancer, cells and cell lines 15 Perou et al. Perou99 26 cDNA (Stanford) Breast cancer Normal breast, breast cancer, human mammary epithelial cells and breast cancer cell lines Differences between breast tissue, cancer, cells and cell lines 16 Pollack et al. Pollack99 10 cDNA (Stanford) 17 Pomeroy et al. Pomeroy02 90 HuGeneFL (Affymetrix) Neuro tumors Central nervous system. Embryonal tumours: medulloblastomas, primitive neuroectodermal tumors (PNETs), atypical teratoid/rhabdoid tumors, and malignant gliomas Differences between different neurological tumors, mostly embryonal 18 Ramaswamy et al. Ramaswamy01 155 HuGeneFL (Affymetrix) Various tumors Large variety of tumors and normal tissues Differences between various tumors and normal tissues 19 Rosenwald et al. Rosenwald01 102 cDNA (Stanford) B lymphoma B cell lymphomas Differences between various B lymphomas 20 Ross et al. Ross00 68 cDNA (Stanford) NCI60 NCI cell lines Differences between the various NCI cell lines 21 Ross et al. Ross01 24 cDNA (Stanford) NCI60 NCI cell lines Differences between the various NCI cell lines 22 Shipp et al. Shipp02 77 HuGeneFL (Affymetrix) B lymphoma B cell lymphomas Differences between various B lymphomas 23 Singh et al. Singh02 102 Hu95 (Affymetrix) Prostate cancer Normal prostate and prostate cancer Differences between prostate cancer and normal prostate 24 Sorlie et al. Sorlie01 85 cDNA (Stanford) Breast cancer Normal breast and breast cancer Differences between different breast carcinomas 25 Stuanton et al. Staunton01 60 HuGeneFL (Affymetrix) NCI60 NCI cell lines Differences between the various NCI cell lines 26 Whitfield et al. Whitfield02 114 cDNA (Stanford) HeLa cell cycle HeLa Cell cycle Differences between the various stages of the HeLa cell cycle